1 Set working dir

## [1] "Current working directory: C:/Users/flyku/Documents/GitHub/NOTCH1-scRNAseq/rmarkdown"

2 Load data

3 Dimension reduction

Here we only want to visualize the sample differences in one UMAP. We adjusted UMAP neighbors and distance paramsters to make the visualization more ‘spread’

## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 25000
## Number of edges: 900161
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.9691
## Number of communities: 15
## Elapsed time: 3 seconds

4 2D

5 3D

6 Session info

## R version 4.1.0 (2021-05-18)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19042)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=Chinese (Simplified)_China.936 
## [2] LC_CTYPE=Chinese (Simplified)_China.936   
## [3] LC_MONETARY=Chinese (Simplified)_China.936
## [4] LC_NUMERIC=C                              
## [5] LC_TIME=Chinese (Simplified)_China.936    
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] plotly_4.9.4.1     Polychrome_1.3.1   qs_0.25.1          here_1.0.1        
##  [5] patchwork_1.1.1    ggplot2_3.3.5      dplyr_1.0.6        cowplot_1.1.1     
##  [9] SeuratObject_4.0.2 Seurat_4.0.4      
## 
## loaded via a namespace (and not attached):
##   [1] Rtsne_0.15            colorspace_2.0-1      deldir_0.2-10        
##   [4] ellipsis_0.3.2        ggridges_0.5.3        rprojroot_2.0.2      
##   [7] spatstat.data_2.1-0   farver_2.1.0          leiden_0.3.9         
##  [10] listenv_0.8.0         ggrepel_0.9.1         RSpectra_0.16-0      
##  [13] fansi_0.5.0           codetools_0.2-18      splines_4.1.0        
##  [16] knitr_1.33            polyclip_1.10-0       jsonlite_1.7.2       
##  [19] ica_1.0-2             cluster_2.1.2         png_0.1-7            
##  [22] uwot_0.1.10           shiny_1.6.0           sctransform_0.3.2    
##  [25] spatstat.sparse_2.0-0 compiler_4.1.0        httr_1.4.2           
##  [28] assertthat_0.2.1      Matrix_1.3-4          fastmap_1.1.0        
##  [31] lazyeval_0.2.2        later_1.2.0           htmltools_0.5.1.1    
##  [34] tools_4.1.0           igraph_1.2.6          gtable_0.3.0         
##  [37] glue_1.4.2            RANN_2.6.1            reshape2_1.4.4       
##  [40] Rcpp_1.0.7            scattermore_0.7       jquerylib_0.1.4      
##  [43] vctrs_0.3.8           nlme_3.1-152          crosstalk_1.1.1      
##  [46] lmtest_0.9-38         xfun_0.25             stringr_1.4.0        
##  [49] globals_0.14.0        mime_0.10             miniUI_0.1.1.1       
##  [52] lifecycle_1.0.0       irlba_2.3.3           goftest_1.2-2        
##  [55] future_1.22.1         MASS_7.3-54           zoo_1.8-9            
##  [58] scales_1.1.1          spatstat.core_2.1-2   promises_1.2.0.1     
##  [61] spatstat.utils_2.2-0  parallel_4.1.0        RColorBrewer_1.1-2   
##  [64] yaml_2.2.1            reticulate_1.20       pbapply_1.4-3        
##  [67] gridExtra_2.3         sass_0.4.0            rpart_4.1-15         
##  [70] stringi_1.6.1         highr_0.9             rlang_0.4.11         
##  [73] pkgconfig_2.0.3       matrixStats_0.60.1    evaluate_0.14        
##  [76] lattice_0.20-44       ROCR_1.0-11           purrr_0.3.4          
##  [79] tensor_1.5            labeling_0.4.2        htmlwidgets_1.5.3    
##  [82] tidyselect_1.1.1      parallelly_1.27.0     RcppAnnoy_0.0.18     
##  [85] plyr_1.8.6            magrittr_2.0.1        R6_2.5.1             
##  [88] generics_0.1.0        DBI_1.1.1             pillar_1.6.2         
##  [91] withr_2.4.2           mgcv_1.8-36           fitdistrplus_1.1-5   
##  [94] scatterplot3d_0.3-41  survival_3.2-11       abind_1.4-5          
##  [97] tibble_3.1.2          future.apply_1.8.1    crayon_1.4.1         
## [100] KernSmooth_2.23-20    utf8_1.2.1            RApiSerialize_0.1.0  
## [103] spatstat.geom_2.2-0   rmarkdown_2.10        grid_4.1.0           
## [106] data.table_1.14.0     digest_0.6.27         xtable_1.8-4         
## [109] tidyr_1.1.3           httpuv_1.6.1          RcppParallel_5.1.4   
## [112] stringfish_0.15.2     munsell_0.5.0         viridisLite_0.4.0    
## [115] bslib_0.2.5.1